4bxf

From Proteopedia

(Difference between revisions)

Current revision

60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment

Structural highlights

4bxf is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIOX2_HUMAN Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Is involved in the demethylation of trimethylated 'Lys-9' on histone H3 (H3K9me3), leading to an increase in ribosomal RNA expression. Also catalyzes the hydroxylation of 60S ribosomal protein L27a on 'His-39'. May play an important role in cell growth and survival. May be involved in ribosome biogenesis, most likely during the assembly process of pre-ribosomal particles.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components and in the hydroxylation of transcription factors and splicing factor proteins. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA and ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone Nepsilon-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases.

Ribosomal oxygenases are structurally conserved from prokaryotes to humans.,Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JR, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ Nature. 2014 May 11. doi: 10.1038/nature13263. PMID:24814345^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tsuneoka M, Koda Y, Soejima M, Teye K, Kimura H. A novel myc target gene, mina53, that is involved in cell proliferation. J Biol Chem. 2002 Sep 20;277(38):35450-9. Epub 2002 Jun 28. PMID:12091391 doi:10.1074/jbc.M204458200
↑ Teye K, Tsuneoka M, Arima N, Koda Y, Nakamura Y, Ueta Y, Shirouzu K, Kimura H. Increased expression of a Myc target gene Mina53 in human colon cancer. Am J Pathol. 2004 Jan;164(1):205-16. PMID:14695334
↑ Tsuneoka M, Fujita H, Arima N, Teye K, Okamura T, Inutsuka H, Koda Y, Shirouzu K, Kimura H. Mina53 as a potential prognostic factor for esophageal squamous cell carcinoma. Clin Cancer Res. 2004 Nov 1;10(21):7347-56. PMID:15534111 doi:10/21/7347
↑ Eilbracht J, Kneissel S, Hofmann A, Schmidt-Zachmann MS. Protein NO52--a constitutive nucleolar component sharing high sequence homologies to protein NO66. Eur J Cell Biol. 2005 Mar;84(2-3):279-94. PMID:15819408
↑ Zhang Y, Lu Y, Yuan BZ, Castranova V, Shi X, Stauffer JL, Demers LM, Chen F. The Human mineral dust-induced gene, mdig, is a cell growth regulating gene associated with lung cancer. Oncogene. 2005 Jul 21;24(31):4873-82. PMID:15897898 doi:1208668
↑ Kuratomi K, Yano H, Tsuneoka M, Sakamoto K, Kusukawa J, Kojiro M. Immunohistochemical expression of Mina53 and Ki67 proteins in human primary gingival squamous cell carcinoma. Kurume Med J. 2006;53(3-4):71-8. PMID:17317935
↑ Lu Y, Chang Q, Zhang Y, Beezhold K, Rojanasakul Y, Zhao H, Castranova V, Shi X, Chen F. Lung cancer-associated JmjC domain protein mdig suppresses formation of tri-methyl lysine 9 of histone H3. Cell Cycle. 2009 Jul 1;8(13):2101-9. Epub 2009 Jul 5. PMID:19502796
↑ Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, McCullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat Chem Biol. 2012 Dec;8(12):960-2. doi: 10.1038/nchembio.1093. Epub 2012 Oct, 28. PMID:23103944 doi:10.1038/nchembio.1093
↑ Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JR, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ. Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature. 2014 May 11. doi: 10.1038/nature13263. PMID:24814345 doi:http://dx.doi.org/10.1038/nature13263

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4bxf"

Categories: Homo sapiens | Large Structures | Chowdhury R | Schofield CJ

@@ Line 1: / Line 1: @@
 ==60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment==
-<StructureSection load='4bxf' size='340' side='right' caption='[[4bxf]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='4bxf' size='340' side='right'caption='[[4bxf]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4bxf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BXF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4bxf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BXF FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xdv|2xdv]], [[4bu2|4bu2]], [[4ccj|4ccj]], [[4cck|4cck]], [[4ccm|4ccm]], [[4ccn|4ccn]], [[4cco|4cco]], [[4diq|4diq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4bxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bxf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bxf RCSB], [http://www.ebi.ac.uk/pdbsum/4bxf PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4bxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bxf OCA], [https://pdbe.org/4bxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bxf RCSB], [https://www.ebi.ac.uk/pdbsum/4bxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bxf ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIOX2_HUMAN RIOX2_HUMAN] Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Is involved in the demethylation of trimethylated 'Lys-9' on histone H3 (H3K9me3), leading to an increase in ribosomal RNA expression. Also catalyzes the hydroxylation of 60S ribosomal protein L27a on 'His-39'. May play an important role in cell growth and survival. May be involved in ribosome biogenesis, most likely during the assembly process of pre-ribosomal particles.<ref>PMID:12091391</ref> <ref>PMID:14695334</ref> <ref>PMID:15534111</ref> <ref>PMID:15819408</ref> <ref>PMID:15897898</ref> <ref>PMID:17317935</ref> <ref>PMID:19502796</ref> <ref>PMID:23103944</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 13: / Line 16: @@
 Ribosomal oxygenases are structurally conserved from prokaryotes to humans.,Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JR, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ Nature. 2014 May 11. doi: 10.1038/nature13263. PMID:24814345<ref>PMID:24814345</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4bxf" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Chowdhury, R.]]
+[[Category: Homo sapiens]]
-[[Category: Schofield, C J.]]
+[[Category: Large Structures]]
-[[Category: Beta-hydroxylation]]
+[[Category: Chowdhury R]]
-[[Category: Dioxygenase]]
+[[Category: Schofield CJ]]
-[[Category: Dsbh]]
-[[Category: Iron-binding]]
-[[Category: Jmjc domain]]
-[[Category: Non-heme]]
-[[Category: Nuclear protein]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase-translation complex]]
-[[Category: Ribosome biogenesis]]
-[[Category: Signaling]]
-[[Category: Transcription and epigenetic regulation]]

4bxf

From Proteopedia

Current revision

60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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